THIS ENTRY 5TMC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SMYSF ORIGINAL DATA ...THIS ENTRY 5TMC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SMYSF ORIGINAL DATA DETERMINED BY AUTHOR: I.ARTSIMOVITCH,V.PATLAN,S.SEKINE,M.N.VASSYLYEVA,T.HOSAKA, K.OCHI,S.YOKOYAMA,D.G.VASSYLYEV,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI).
Resolution: 2.71→48.51 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. L-test and other twinning statistical tests have shown that the 1SMY data were partially twinned, but not perfectly twinned. With partial ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. L-test and other twinning statistical tests have shown that the 1SMY data were partially twinned, but not perfectly twinned. With partial twinning, the symmetry is partially upshifted to P6(5)22 from P6(5), which is consistent with the observed systematic absences and intensity merging R-factors reported for them. If the correct space group were P3(2), an up-shifted symmetry by a different twinning operation along the 3-fold axis could only generate P6(4), but not P6(5) because P3(2) is not a subgroup of P6(5). Moreover, the conversion of P3(2) to P6(5) using a perfect twinning method is not consistent with the L-test results, either, which suggests only a partial twinning, not perfect twinning. Given the problem of partial twinning in the data, model refinement was indeed very challenging. Six independent attempts of model refinement were made after proper crystallographic origin shift, starting with six different partial models according to the notes in author's notebook. All appear to have converged to similar crystallographic R-factor and free R-factor, even though the number of atoms in the final coordinates varied slightly among them. At the time of submission of this entry, the files for two of the six attempts have been located, but the remaining four files have not. It appears that there might be a mix-up in number of atoms among these files when reporting the number of atoms and R-factors.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2864
7528
3.7 %
RANDOM
Rwork
0.2651
-
-
-
obs
0.26588
198576
96.94 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK